As said earlier, it takes a planetary sized network for an AI to go rampant. Durandal had the Marathon's network, which was huge. Now in order for Cortana to begin rampancy, she would need a huge network. That huge network would be the Forerunner's. Being in there for that long she undoubtedly had enough time to see every secret the Forerunner had.

And another clue to Cortana not being so nice anymore. We all know how she already resents humans, especialy marines. She always underestimates them, presuming they are dead when they're not. And when she has to open the locked door aboard the T&R, she is mad because a marine told her to hurry up, and she says she would like to see him do that very quietly.

Now if Cortana wanted to help MC stop the flood and 343 GS, why didn't she go with him to stop Keyes? She couldn't spare a few seconds for MC to pull her out of the core and back into MC? No doubt she could help him immensely with figuring out 343's true intentions. But could she get the index if she had gone with MC? I don't think so. She only got the index because 343 didn't know about her and he gave the index to MC to put into the core, and she intercepted it. So she stayed in the core to get the index.

It is my opinion that the index holds more power than just activating Halo, and Cortana knew that before sending MC to stop Keyes. She knew it could help her with other motive she has.